Pre-Note : 1993 Honda Civic Si Hatch w/o ABS, w/ Nissin Rear Brakes

I was replacing the rear brake pads when i noticed my right rear caliper was rusted to a stop and then went ahead and replaced and bled both rear calipers/pads. Now I'm a bit confused on how the caliper is supposed to be compressed, i've tried normally a few times, but it says in the haynes manual to line the cross up with the tab on the brake pad, is this the tiny dot that sticks up? And if so, could this be the reason my e-brake is not working whatsoever? Is there a way to adjust the e-brake, because i'm assuming that has something to do with that problem. Any help is great!